diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/set_nd.Rd | 64 | ||||
| -rw-r--r-- | man/set_nd_nq.Rd | 103 |
2 files changed, 103 insertions, 64 deletions
diff --git a/man/set_nd.Rd b/man/set_nd.Rd deleted file mode 100644 index cef2705..0000000 --- a/man/set_nd.Rd +++ /dev/null @@ -1,64 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/set_nd.R -\name{set_nd} -\alias{set_nd} -\alias{set_nd_focus} -\title{Set non-detects in residue series without replicates} -\usage{ -set_nd(r, lod, loq = NA, time_zero = TRUE, time_zero_nd_value = NA, - stop_after_first_nondetect = FALSE) - -set_nd_focus(r, lod, loq = NA, time_zero = TRUE) -} -\arguments{ -\item{r}{A character vector of sequential residues without replicates, with -non-detects specified as 'nd' and unquantified values above the limit of -detection specified as 'nq', otherwise coercible to numeric} - -\item{lod}{Limit of detection (numeric)} - -\item{loq}{Limit of quantification(numeric). Must be specified if the FOCUS rule to -stop after the first non-detection is to be applied} - -\item{time_zero}{Is the first value in the series a time zero value?} - -\item{time_zero_nd_value}{Which value should we use for non-detects at time zero?} - -\item{stop_after_first_nondetect}{Should we really stop after the first non-detection?} -} -\description{ -Sets non-detects directly before or directly after detects to NA. Values between -lod and loq are set to their mean value if an loq is specified. -If 'time_zero' is set to TRUE, the residue series is assumed to start with time -zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the -set_nd_focus variant, this is zero, otherwise this argument has NA as default -value. -If stopping after the first non-detection is requested, as in in the FOCUS -variant of the function, an loq has to be specified in order to decide -if any later detections are above the loq. -} -\section{Functions}{ -\itemize{ -\item \code{set_nd}: Set non-detects in residues series - -\item \code{set_nd_focus}: Set non-detects in residues series according to FOCUS rules -}} - -\examples{ -# FOCUS (2014) p. 75/76 and 131/132 -parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd") -set_nd(parent_1, 0.02) -parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd") -set_nd(parent_2, 0.02) -set_nd_focus(parent_2, 0.02, loq = 0.05) -parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd") -set_nd(parent_3, 0.02) -set_nd_focus(parent_3, 0.02, loq = 0.05) -metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd") -set_nd(metabolite, 0.02) -} -\references{ -FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation - Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, - 18 December 2014, p. 251 -} diff --git a/man/set_nd_nq.Rd b/man/set_nd_nq.Rd new file mode 100644 index 0000000..b2da429 --- /dev/null +++ b/man/set_nd_nq.Rd @@ -0,0 +1,103 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/set_nd_nq.R +\name{set_nd_nq} +\alias{set_nd_nq} +\alias{set_nd_nq_focus} +\title{Set non-detects and unquantified values in residue series without replicates +This function automates replacing unquantified values in residue time and +depth series. For time series, the function performs part of the residue +processing proposed in the FOCUS kinetics guidance for parent compounds +and metabolites. For two-dimensional residue series over time and depth, +it automates the proposal of Boesten et al (2015).} +\usage{ +set_nd_nq(res_raw, lod, loq = NA, time_zero_presence = FALSE) + +set_nd_nq_focus(res_raw, lod, loq = NA, set_first_sample_nd = TRUE, + first_sample_nd_value = 0, ignore_below_loq_after_first_nd = TRUE) +} +\arguments{ +\item{res_raw}{Character vector of a residue time series, or matrix of +residue values with rows representing depth profiles for a specific sampling +time, and columns representing time series of residues at the same depth. +Values below the limit of detection (lod) have to be coded as "nd", values +between the limit of detection and the limit of quantification, if any, have +to be coded as "nq". Samples not analysed have to be coded as "na". All +values that are not "na", "nd" or "nq" have to be coercible to numeric} + +\item{lod}{Limit of detection (numeric)} + +\item{loq}{Limit of quantification(numeric). Must be specified if the FOCUS rule to +stop after the first non-detection is to be applied} + +\item{time_zero_presence}{Do we assume that residues occur at time zero? +This only affects samples from the first sampling time that have been +reported as "nd" (not detected).} + +\item{set_first_sample_nd}{Should the first sample be set to "first_sample_nd_value" +in case it is a non-detection?} + +\item{first_sample_nd_value}{Value to be used for the first sample if it is a non-detection} + +\item{ignore_below_loq_after_first_nd}{Should we ignore values below the LOQ after the first +non-detection that occurs after the quantified values?} +} +\value{ +A numeric vector, if a vector was supplied, or a numeric matrix otherwise +} +\description{ +Set non-detects and unquantified values in residue series without replicates +This function automates replacing unquantified values in residue time and +depth series. For time series, the function performs part of the residue +processing proposed in the FOCUS kinetics guidance for parent compounds +and metabolites. For two-dimensional residue series over time and depth, +it automates the proposal of Boesten et al (2015). +} +\section{Functions}{ +\itemize{ +\item \code{set_nd_nq_focus}: Set non-detects in residue time series according to FOCUS rules +}} + +\examples{ +# FOCUS (2014) p. 75/76 and 131/132 +parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd") +set_nd_nq(parent_1, 0.02) +parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd") +set_nd_nq(parent_2, 0.02) +set_nd_nq_focus(parent_2, 0.02, loq = 0.05) +parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd") +set_nd_nq(parent_3, 0.02) +set_nd_nq_focus(parent_3, 0.02, loq = 0.05) +metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd") +set_nd_nq(metabolite, 0.02) +set_nd_nq_focus(metabolite, 0.02, 0.05) +# +# Boesten et al. (2015), p. 57/58 +table_8 <- matrix( + c(10, 10, rep("nd", 4), + 10, 10, rep("nq", 2), rep("nd", 2), + 10, 10, 10, "nq", "nd", "nd", + "nq", 10, "nq", rep("nd", 3), + "nd", "nq", "nq", rep("nd", 3), + rep("nd", 6), rep("nd", 6)), + ncol = 6, byrow = TRUE) +set_nd_nq(table_8, 0.5, 1.5, time_zero_presence = TRUE) +table_10 <- matrix( + c(10, 10, rep("nd", 4), + 10, 10, rep("nd", 4), + 10, 10, 10, rep("nd", 3), + "nd", 10, rep("nd", 4), + rep("nd", 18)), + ncol = 6, byrow = TRUE) +set_nd_nq(table_10, 0.5, time_zero_presence = TRUE) +} +\references{ +Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H. +J. and Pol, J. W. (2015). Leaching of plant protection products and their +transformation products; Proposals for improving the assessment of leaching +to groundwater in the Netherlands — Version 2. Alterra report 2630, Alterra +Wageningen UR (University & Research centre) + +FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation + Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, + 18 December 2014, p. 251 +} |